instructions_SF6.txt

#Set the "Scripts" directory as working directory in RStudio by navigating within the bottom right "Files" panel, then press "Set As Working directory" under "More". 
#Do this before executing any of the R scripts mentioned below.

## Run the following commands from RStudio Console:
source("diffBUM_HMM_35S_dataset.R")
source("diffBUM_HMM_35S_dataset_scaled_DORs.R")
source("dStruct_35S_dataset.R")
source("script_creating_SHAPE_map_files_35S_dataset.R")

## Run the following commands from within an environment (e.g. virtual environment created with conda or virtualenv) with Python 2.7 installed:
pip install matplotlib.pyplot
pip install numpy 
pip install scipy
python deltaSHAPE.py 35s_delta5_rep1.map 35s_deltaerb1_rep1.map -o "35S_deltaerb1_Vs_delta5_reps1.txt "
python deltaSHAPE.py 35s_delta5_rep2.map 35s_deltaerb1_rep2.map -o "35S_deltaerb1_Vs_delta5_reps2.txt "